VMD-L Mailing List
From: Cun Zhang (apzc2529_at_gmail.com)
Date: Mon Sep 27 2010 - 20:17:33 CDT
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try to add pbc parameter when using trjconv, it may be mol or res,say
trjconv -pbc mol .....
For more information, run command 'trjconv -h', and the '-pbc' part in the
help.
On Mon, Sep 27, 2010 at 5:58 PM, Joyce Tan <joyce.tankh_at_gmail.com> wrote:
> Hi.
>
> I've extended my 5ns MD simulation for another 10ns using GROMACS. After
> the simulation completed, i've converted some of the trajectory frame into
> pdb format and the protein appear to break into parts as in the attached
> jpeg file. When I look back to the trajectory file, the protein is broken
> into parts, too with long lines connecting the parts. May I know why this
> occur and how to solve it?
>
> Thanks.
>
> Regards,
> Joyce
>
-- Blog: http://www.edwardpku.com/cun
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